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AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement

Authors :
Lawrence Chai
Ping Zhu
Jin Chai
Changxu Pang
Babak Andi
Sean McSweeney
John Shanklin
Qun Liu
Source :
Crystals, Vol 11, Iss 10, p 1227 (2021)
Publication Year :
2021
Publisher :
MDPI AG, 2021.

Abstract

Crystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a commonly used phasing method for crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database to find suitable templates for phasing. However, sequence information is not always available, such as when proteins are crystallized with unknown binding partner proteins or when the crystal is of a contaminant. The recent development of AlphaFold published the predicted protein structures for every protein from twenty distinct species. In this work, we tested whether AlphaFold-predicted E. coli protein structures were accurate enough to enable sequence-independent phasing of diffraction data from two crystallization contaminants of unknown sequence. Using each of more than 4000 predicted structures as a search model, robust molecular replacement solutions were obtained, which allowed the identification and structure determination of YncE and YadF. Our results demonstrate the general utility of the AlphaFold-predicted structure database with respect to sequence-independent crystallographic phasing.

Details

Language :
English
ISSN :
20734352
Volume :
11
Issue :
10
Database :
Directory of Open Access Journals
Journal :
Crystals
Publication Type :
Academic Journal
Accession number :
edsdoj.5e512db4ab14c538cb8a428afc3f4f0
Document Type :
article
Full Text :
https://doi.org/10.3390/cryst11101227